[gmx-users] Re: Seeking solution for the error "Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms".

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Sep 17 06:23:40 CEST 2013

Hi Santhosh,

Try renaming the atom (mind the space):

sed 's/OXT/O2 /' pdbfile > fixed.pdb

And then run pdb2gmx on that.



On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan <
santhoshrajan90 at gmail.com> wrote:

> This is the command I used
> pdb2gmx -f protein.pdb -o processed.gro -water spce -ignh
> And I used OPLS-AA/L all-atom force field..
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Tsjerk A. Wassenaar, Ph.D.

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